Andrea's note on Micro resulting - Healthedata1/OO-on-FHIR-Micro-Profile GitHub Wiki

A bit delayed to the thread. Per the question about organism identified.

It does vary by LIS & EHR vendor and laboratory by what they support and how they structure their culture based results reporting. Some vendors are able to support and laboratories structure laboratory orders and results in the following manner:

  1.    Lab Order:  Culture, Blood  (mapped to LOINC to meet OBR-4 requirements)

  2.   Lab Result:  Organism#1  identified:  (no LOINC code for this phrase/meaning, unless folks use the same one for the order to meet OBX 3 requirements)

  3.   Lab Result Value:  Staphylococcus aureus  (mapped to SCT organism code to meet OBX 5  requirement)

Additionally, additional orders and results are “added” on by the laboratory to document tasks/workflows performed and to charge for the additional work, and communicate to the ordering provider and public health the additional information concerning the organism/specimen. The ELR guide appears to indicate it’s up to the laboratory to whether they report each OBR-4 OBX3 order & result pair for each kind of add on to the specimen. It could be due to recording isolate identification, susceptibility testing, other testing such as oxidase, catalase, etc. Similar patterns occur in blood bank as the ordering provider is unaware upon order which organisms, antibodies, etc will be present in the specimen, so should be aligned with LRI as part of the harmonization project.

  1.   Lab Order:  Gram Positive bacteria susceptibility panel (sent in OBR-4 and would need to be mapped to LOINC to meet terminology requirements)

  2.   Lab Result:  Methicillin  (mapped to LOINC to meet OBX 3 requirements. Public health and others do want specific details such as methodology, MIC, etest, etc, which is needed for analytics and population health downstream).

  3.   Lab Result Value:  Resistant (mapped to SCT qualifier value to meet OBX-5 requirements)  May also be numeric MIC result value, which has no coding in OBX -5, but would require an “interpretation” code such as “R” from HL7 0078 table placed in OBX -8.  Laboratories will typically report one way or the other and it seems split across  laboratory medicine.

That said, there are a number of EHR and LIS vendors cannot support the functionality above and thus the end user has structured their culture data differently. The differences typically manifest as the following:

  1.   Lab Order:  Culture, Blood  (mapped to LOINC to meet OBR-4 requirements)

  2.   OBX 5:  Staphylococcus aureus    (or potentially the MRSA pre-coordinated SCT organism code, which really shouldn’t be used as it would cause duplication encoding and work.  Rather the post-coordinated approach of LOINC encoding the antibiotic, SCT encoding the organism, and SCT encoding the resistant in OBX 5 or using the HL7 0078 R code in OBX 8, would provide the receiver the information if they can process post coordinated message.

Not only is there the interface check issue, for results sent to reference/external labs, the results coming in shouldn’t be altered coming back into the LIS and sent to downstream entities to meet another requirement (my summary, folks can look up the details.)

The LOINC names should not be used for any of the original/local name from the performing lab or downstream entities for display, but rather mapped and sent in one of the triplets, for confirming correct mapping with the human readable name (would like to see the LOINC Long Name required as the short name is too ambiguous, is blank in a number of occasions, and can cause patient safety issues.) Functionality varies on which is sent with the LOINC code in the message as well. Important as the descriptions often vary depending on the LOINC release due to a large number of changes by Regenstrief as they update their editorial in releases (20,000 changes in June 2016 release alone.)

While different approaches continue, it will mean public health and other downstream end uses will receive the variety of these practices, and interoperability will be more be harder to achieve.

Do support indicating which triplet in CWE will be utilized for interface checks for consistency and so receivers know which triplet to find the original text provided by the performing laboratory which would carry through downstream unaltered. It will help standardize to a single approach that makes communication and understanding of the types of data more clear. Additionally, for those who map other terminologies (to meet other MU requirements such as HAI reporting) in other triplets, it should make it more standardized for receives to know where those data are located as well. Would also think that if this is communicated to CMS laboratory inspectors, it would also facilitate their job in comparing the descriptions if they know to look for the information in the same triplet (although CMS doesn’t require the how the requirements are met, just that they are met.)

Look forward to seeing the updates.